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Amber Herold, 05/31/2011 12:51 PM
Reconstruction Parameters¶
| Name | a.k.a. | Description | Used By | Required in interface? |
|---|---|---|---|---|
| Mask Radius | mask | raduius of external map in pixels | xmipp, eman, imagic | |
| Inner Radius | inner radius for alignment in pixels | xmipp | ||
| imask | Particle inner mask radius | radius of internal mask (in pixels for eman and spider, Angstroms for frealign) | EMAN, frealign, spider | |
| Outer Radius | xmipp | |||
| Particle outer mask radius (RO) | mask | radius from center of particle to outer edge (frealign in angstroms, spider in pixels) | frealign, spider | |
| amask | amask=[r],[threshold],[iter] | eman | ||
| MRA - min radius for rotational alignment in pixels | imagic | |||
| MRA - max radius for rotational alignment in pixels | imagic | |||
| firstring | Any pixels this far away from center will not be used | spider | ||
| lastring | Only pixels this far away will be used | spider | ||
| xysearch | translational search during projection matching will be limited to this many pixels from the center ofthe image | spider | ||
| Symmetry Group | sym | ex. c1, c2... | xmipp,eman,frealign,spider,imagic | |
| Number of iterations | iteration number | xmipp | ||
| Mask Filename | xmipp | |||
| Angular reconstitution | angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep | imagic | ||
| Angular Sampling Rate | xmipp | |||
| Max angular change | xmipp | |||
| max change offset | xmipp | |||
| Search range for 5d transitional search | xmipp | |||
| Discard % of image with CCF below | xmipp | |||
| Reconstruction Method | xmipp | |||
| Values of lambda for ART | xmipp | |||
| Initial max frequency used by reconstruct fourier | xmipp | |||
| Compute resolution? | xmipp | |||
| Low Pass Filter the reference? | xmipp | |||
| Do not use estimated resolution for low-pass filtering? | xmipp | |||
| Constant to add to the estimated resolution | xmipp | |||
| ang | angular step for projections in degrees | EMAN | ||
| angular increments | list of angular increments for projection mapping | spider | ||
| MRA - angular increment of forward projections | imagic | |||
| maxshift | max translation during image alignment in pixels | eman | ||
| xyshift | particles only allowed to shift this far from center | spider | ||
| MRA - max radial shift compared to original images | imagic | |||
| MRA - max radial shift during this iteration | imagic | |||
| hard | hard limit for make3d program | eman | ||
| clskeep | =[std dev multipier] how many raw particles discarded for each class average | eman | ||
| clsiter | iterative alignmnet to each other | eman | ||
| filt3d | applies gaussian low pass filter in pixels [rad] | eman | ||
| xfiles | =[mas in kD] | eman | ||
| Approximate mass in Kd | imagic | |||
| shrink | scale down by a factor of [n] before classification | eman | ||
| euler2 | =[oversample factor] | eman | ||
| median | use median value instead of average for each pixel | eman | ||
| phscls | use signal to noise ratio weighted phase residual | eman | ||
| refine | do subpixel alignment | eman | ||
| tree | decimate reference populatiuon | eman | ||
| coran | use coran algorithm | eman | ||
| eotest | use even odd test | eman | ||
| amplitude contrast (WGH) | frealign | |||
| Standard deviation filtering | fealign | |||
| keep | determines which particles are kept for back-projection, -1 is one standard deviation worse than mean | spider | ||
| MSA - fraction of final class averages to keep | imagic | |||
| Phase B-factor weighting constant (PBC) | frealign | |||
| B-factor offset (BOFF) | frealign | |||
| Number of randomized search trials (ITMAX) | frealign | |||
| Number of potential matches to refine (IPMAX) | frealign | |||
| Target phase residual (TARGET) | frealign | |||
| Worst phase residual for inclusion (THRESH) | frealign | |||
| Resolution limit of reconstruction (RREC) (in Ångstroms; default Nyquist) | frealign | |||
| lp | filtering | low pass filter in angstroms | spider, imagic | |
| hp | filtering | high pass filter in angstroms | spider, imagic | |
| Lower resolution limit or high-pass filter (RMAX1) (in Ångstroms) | frealign | |||
| Higher resolution limit or low-pass filter (RMAX2) (in Ångstroms; default 2*Nyquist) | frealign | |||
| B-factor correction (RBFACT) (0 = off) | frealign | |||
| Only use CTFFIND values | frealign | |||
| Last particle to use | frealign | |||
| MSA - percentage of images to ignore when calculating eiganimages | imagic | |||
| MSA - num class averges to produce from raw images | imagic | |||
| MSA - num factors to use for classification | imagic | |||
| MSA - percentage of worst class members to ignore after classification | imagic | |||
| threed reconstruction | object size, low-pass filter 3d volume | imagic | ||
| Center stack prior to alignment | imagic | |||
| Mirror references for alignment | imagic |
Updated by Amber Herold over 13 years ago · 8 revisions